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Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan
Since its emergence in China, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide including Pakistan. During the pandemic, whole genome sequencing has played an important role in understanding the evolution and genomic diversity of SARS-CoV-2. Although an unprecedented...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7987156/ https://www.ncbi.nlm.nih.gov/pubmed/33755704 http://dx.doi.org/10.1371/journal.pone.0248371 |
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author | Umair, Massab Ikram, Aamer Salman, Muhammad Khurshid, Adnan Alam, Masroor Badar, Nazish Suleman, Rana Tahir, Faheem Sharif, Salmaan Montgomery, Joel Whitmer, Shannon Klena, John |
author_facet | Umair, Massab Ikram, Aamer Salman, Muhammad Khurshid, Adnan Alam, Masroor Badar, Nazish Suleman, Rana Tahir, Faheem Sharif, Salmaan Montgomery, Joel Whitmer, Shannon Klena, John |
author_sort | Umair, Massab |
collection | PubMed |
description | Since its emergence in China, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide including Pakistan. During the pandemic, whole genome sequencing has played an important role in understanding the evolution and genomic diversity of SARS-CoV-2. Although an unprecedented number of SARS-CoV-2 full genomes have been submitted in GISAID and NCBI, data from Pakistan is scarce. We report the sequencing, genomic characterization, and phylogenetic analysis of five SARS-CoV-2 strains isolated from patients in Pakistan. The oropharyngeal swabs of patients that were confirmed positive for SARS-CoV-2 through real-time RT-PCR at National Institute of Health, Pakistan, were selected for whole-genome sequencing. Sequencing was performed using NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEW ENGLAND BioLabs Inc., MA, US) and Illumina iSeq 100 instrument (Illumina, San Diego, US). Based on whole-genome analysis, three Pakistani SARS-CoV-2 strains clustered into the 20A (GH) clade along with the strains from Oman, Slovakia, United States, and Pakistani strain EPI_ISL_513925. The two 19B (S)-clade strains were closely related to viruses from India and Oman. Overall, twenty-nine amino acid mutations were detected in the current study genome sequences, including fifteen missense and four novel mutations. Notably, we have found a D614G (aspartic acid to glycine) mutation in spike protein of the sequences from the GH clade. The G614 variant carrying the characteristic D614G mutation has been shown to be more infectious that lead to its rapid spread worldwide. This report highlights the detection of GH and S clade strains and G614 variant from Pakistan warranting large-scale whole-genome sequencing of strains prevalent in different regions to understand virus evolution and to explore their genetic diversity. |
format | Online Article Text |
id | pubmed-7987156 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-79871562021-04-02 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan Umair, Massab Ikram, Aamer Salman, Muhammad Khurshid, Adnan Alam, Masroor Badar, Nazish Suleman, Rana Tahir, Faheem Sharif, Salmaan Montgomery, Joel Whitmer, Shannon Klena, John PLoS One Research Article Since its emergence in China, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide including Pakistan. During the pandemic, whole genome sequencing has played an important role in understanding the evolution and genomic diversity of SARS-CoV-2. Although an unprecedented number of SARS-CoV-2 full genomes have been submitted in GISAID and NCBI, data from Pakistan is scarce. We report the sequencing, genomic characterization, and phylogenetic analysis of five SARS-CoV-2 strains isolated from patients in Pakistan. The oropharyngeal swabs of patients that were confirmed positive for SARS-CoV-2 through real-time RT-PCR at National Institute of Health, Pakistan, were selected for whole-genome sequencing. Sequencing was performed using NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEW ENGLAND BioLabs Inc., MA, US) and Illumina iSeq 100 instrument (Illumina, San Diego, US). Based on whole-genome analysis, three Pakistani SARS-CoV-2 strains clustered into the 20A (GH) clade along with the strains from Oman, Slovakia, United States, and Pakistani strain EPI_ISL_513925. The two 19B (S)-clade strains were closely related to viruses from India and Oman. Overall, twenty-nine amino acid mutations were detected in the current study genome sequences, including fifteen missense and four novel mutations. Notably, we have found a D614G (aspartic acid to glycine) mutation in spike protein of the sequences from the GH clade. The G614 variant carrying the characteristic D614G mutation has been shown to be more infectious that lead to its rapid spread worldwide. This report highlights the detection of GH and S clade strains and G614 variant from Pakistan warranting large-scale whole-genome sequencing of strains prevalent in different regions to understand virus evolution and to explore their genetic diversity. Public Library of Science 2021-03-23 /pmc/articles/PMC7987156/ /pubmed/33755704 http://dx.doi.org/10.1371/journal.pone.0248371 Text en https://creativecommons.org/publicdomain/zero/1.0/ This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 (https://creativecommons.org/publicdomain/zero/1.0/) public domain dedication. |
spellingShingle | Research Article Umair, Massab Ikram, Aamer Salman, Muhammad Khurshid, Adnan Alam, Masroor Badar, Nazish Suleman, Rana Tahir, Faheem Sharif, Salmaan Montgomery, Joel Whitmer, Shannon Klena, John Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan |
title | Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan |
title_full | Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan |
title_fullStr | Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan |
title_full_unstemmed | Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan |
title_short | Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan |
title_sort | whole-genome sequencing of sars-cov-2 reveals the detection of g614 variant in pakistan |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7987156/ https://www.ncbi.nlm.nih.gov/pubmed/33755704 http://dx.doi.org/10.1371/journal.pone.0248371 |
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